SPATA32

spermatogenesis associated 32

Basic information

Region (hg38): 17:45254393-45262094

Previous symbols: [ "C17orf46", "TEX34" ]

Links

ENSG00000184361 ∙ NCBI:124783 ∙ ∙ HGNC:26349 ∙ Uniprot:Q96LK8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA32 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA32 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in SPATA32

This is a list of pathogenic ClinVar variants found in the SPATA32 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-45254488-C-T		not specified	Uncertain significance (Sep 10, 2024)
17-45255208-C-T		not specified	Uncertain significance (Dec 10, 2024)
17-45255213-G-T		not specified	Uncertain significance (Jul 12, 2022)
17-45255322-C-T		not specified	Likely benign (Nov 21, 2024)
17-45255338-T-C		not specified	Uncertain significance (Feb 12, 2024)
17-45255347-G-A		not specified	Uncertain significance (Feb 16, 2023)
17-45255350-C-G		not specified	Uncertain significance (Aug 20, 2024)
17-45255374-G-C		not specified	Uncertain significance (Aug 02, 2022)
17-45255392-T-A		not specified	Uncertain significance (Sep 11, 2024)
17-45255406-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-45255409-A-G		not specified	Uncertain significance (Sep 11, 2024)
17-45255430-G-A		not specified	Uncertain significance (May 09, 2024)
17-45255542-A-T		not specified	Uncertain significance (Aug 12, 2021)
17-45255572-C-T		not specified	Likely benign (Dec 15, 2022)
17-45255599-C-G		not specified	Uncertain significance (Nov 20, 2024)
17-45255623-G-C		not specified	Uncertain significance (Mar 28, 2023)
17-45255662-C-T		not specified	Uncertain significance (Aug 26, 2024)
17-45255704-C-A		not specified	Uncertain significance (Nov 13, 2023)
17-45255716-G-A		not specified	Uncertain significance (Nov 20, 2023)
17-45255772-G-A		not specified	Uncertain significance (Dec 03, 2024)
17-45255779-T-G		not specified	Uncertain significance (Jan 24, 2024)
17-45255781-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-45255805-G-T		not specified	Likely benign (Aug 22, 2023)
17-45255848-C-T		not specified	Uncertain significance (Jun 16, 2023)
17-45255888-G-C		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA32	protein_coding	protein_coding	ENST00000331780	5	7720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-9	0.109	125729	0	9	125738	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.584	184	208	0.886	0.0000121	2505
Missense in Polyphen		33	40.929	0.80627		520
Synonymous	0.678	82	90.2	0.909	0.00000597	769
Loss of Function	0.154	14	14.6	0.957	7.22e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0711

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.123
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Spata32

Gene ontology

• Biological process: spermatogenesis
• Cellular component: perinuclear region of cytoplasm
• Molecular function: actin binding